BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231839.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 2,131,391 number of mapped reads = 1,964,759 (92.18%) number of supplementary alignments = 14,132 (0.66%) number of secondary alignments = 0 number of mapped bases = 131,747,208 bp number of sequenced bases = 131,685,438 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 130,951 duplication rate = 4.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.8839 >>>>>>> ACTG content number of A's = 36,512,236 bp (27.73%) number of C's = 24,516,679 bp (18.62%) number of T's = 41,214,876 bp (31.3%) number of G's = 29,392,779 bp (22.32%) number of N's = 48,868 bp (0.04%) GC percentage = 40.94% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,076,641 number of insertions = 10,508 mapped reads with insertion percentage = 0.53% number of deletions = 33,600 mapped reads with deletion percentage = 1.69% homopolymer indels = 44.24% >>>>>>> Coverage mean coverageData = 0.0426X std coverageData = 0.7876X There is a 3.69% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 14493080 0.05814661541003743 2.0623626310354415 chr2 243199373 10277892 0.04226117803354699 0.5940627307864164 chr3 198022430 15056649 0.07603506835059039 0.31823586894129796 chr4 191154276 6482124 0.03391043159296107 0.22582734289682513 chr5 180915260 6994026 0.03865912693047563 0.23172536999987767 chr6 171115067 7405518 0.04327800076190836 0.3919983348250083 chr7 159138663 9021736 0.056691038054027136 1.1903229383386649 chr8 146364022 6383206 0.04361185155187933 0.8101837782856809 chr9 141213431 5616486 0.039773029804792435 0.5294535464421841 chr10 135534747 5899373 0.043526646344055224 0.7325871883209978 chr11 135006516 6246052 0.04626481880326428 0.49367417303515515 chr12 133851895 3923453 0.029311897302611967 0.2144780784480309 chr13 115169878 3588244 0.031156097951236868 0.19420977708578216 chr14 107349540 5268378 0.04907685678019673 0.30434243361270547 chr15 102531392 2278545 0.022222901255451597 0.1787761605859563 chr16 90354753 3086336 0.03415798170573273 0.3124632305455615 chr17 81195210 3031225 0.037332559396053046 0.29035062988525767 chr18 78077248 3046620 0.039020586381323275 1.1768958347704028 chr19 59128983 3748446 0.06339439323690042 1.1066825312908397 chr20 63025520 2340244 0.037131688877775224 0.24414094557005786 chr21 48129895 2065526 0.04291565564396099 0.25933732671952975 chr22 51304566 1133895 0.022101249233840124 0.16077452167129808 chrMT 16571 65276 3.9391708406251884 3.273380449821947 chrX 155270560 3964900 0.025535426677149874 0.2722109881527737 chrY 59373566 329978 0.005557658436752814 0.12849065348568622